/* *****************************************************************
    MESQUITE -- The Mesh Quality Improvement Toolkit

    Copyright 2004 Lawrence Livermore National Laboratory.  Under
    the terms of Contract B545069 with the University of Wisconsin --
    Madison, Lawrence Livermore National Laboratory retains certain
    rights in this software.

    This library is free software; you can redistribute it and/or
    modify it under the terms of the GNU Lesser General Public
    License as published by the Free Software Foundation; either
    version 2.1 of the License, or (at your option) any later version.

    This library is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
    Lesser General Public License for more details.

    You should have received a copy of the GNU Lesser General Public License
    (lgpl.txt) along with this library; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

    kraftche@cae.wisc.edu

  ***************************************************************** */

#include "MeshImplData.hpp"
#include "TopologyInfo.hpp"
#include "MsqError.hpp"

// NOTE: If this is defined, the normal vertex query functions
//       will not return mid-nodes.
#undef SEPARATE_MID_NODES

namespace MBMesquite
{

const std::vector< size_t > dummy_list;
const Vector3D dummy_vtx;

size_t MeshImplData::num_vertices() const
{
    size_t count = 0;
    for( std::vector< Vertex >::const_iterator iter = vertexList.begin(); iter != vertexList.end(); ++iter )
#ifdef SEPARATE_MID_NODES
        if( iter->valid && iter->midcount < iter->adjacencies.size() )
#else
        if( iter->valid )
#endif
            ++count;
    return count;
}

size_t MeshImplData::num_elements() const
{
    return elementList.size() - deletedElementList.size();
}

size_t MeshImplData::num_vertex_uses() const
{
    size_t result = 0;
    for( std::vector< Element >::const_iterator iter = elementList.begin(); iter != elementList.end(); ++iter )
    {
#ifdef SEPARATE_MID_NODES
        unsigned from_topo = TopologyInfo::corners( iter->topology );
        result += from_topo ? from_topo : iter->connectivity.size();
#else
        result += iter->connectivity.size();
#endif
    }
    return result;
}

const Vector3D& MeshImplData::get_vertex_coords( size_t index, MsqError& err ) const
{
    if( !is_vertex_valid( index ) )
    {
        MSQ_SETERR( err )( "Invalid vertex handle", MsqError::INVALID_ARG );
        return dummy_vtx;
    }

    return vertexList[index].coords;
}

bool MeshImplData::vertex_is_fixed( size_t index, MsqError& err ) const
{
    if( !is_vertex_valid( index ) )
    {
        MSQ_SETERR( err )( "Invalid vertex handle", MsqError::INVALID_ARG );
        return false;
    }

    return vertexList[index].fixed;
}

bool MeshImplData::vertex_is_slaved( size_t index, MsqError& err ) const
{
    if( !is_vertex_valid( index ) )
    {
        MSQ_SETERR( err )( "Invalid vertex handle", MsqError::INVALID_ARG );
        return false;
    }
    if( !have_slaved_flags() )
    {
        MSQ_SETERR( err )( "Slave flags not set", MsqError::INVALID_STATE );
        return false;
    }

    return vertexList[index].slaved;
}

void MeshImplData::fix_vertex( size_t index, bool flag, MsqError& err )
{
    if( !is_vertex_valid( index ) )
    {
        MSQ_SETERR( err )( "Invalid vertex handle", MsqError::INVALID_ARG );
        return;
    }

    vertexList[index].fixed = flag;
}

void MeshImplData::slave_vertex( size_t index, bool flag, MsqError& err )
{
    if( !is_vertex_valid( index ) )
    {
        MSQ_SETERR( err )( "Invalid vertex handle", MsqError::INVALID_ARG );
        return;
    }

    vertexList[index].slaved = flag;
    haveSlavedFlags          = true;
}

unsigned char MeshImplData::get_vertex_byte( size_t index, MsqError& err ) const
{
    if( !is_vertex_valid( index ) )
    {
        MSQ_SETERR( err )( "Invalid vertex handle", MsqError::INVALID_ARG );
        return 0;
    }

    return vertexList[index].byte;
}

void MeshImplData::set_vertex_byte( size_t index, unsigned char value, MsqError& err )
{
    if( !is_vertex_valid( index ) )
    {
        MSQ_SETERR( err )( "Invalid vertex handle", MsqError::INVALID_ARG );
        return;
    }

    vertexList[index].byte = value;
}

EntityTopology MeshImplData::element_topology( size_t index, MsqError& err ) const
{
    if( !is_element_valid( index ) )
    {
        MSQ_SETERR( err )( "Invalid element handle", MsqError::INVALID_ARG );
        return MIXED;
    }

    return elementList[index].topology;
}

void MeshImplData::element_topology( size_t index, EntityTopology type, MsqError& err )
{
    if( !is_element_valid( index ) )
    {
        MSQ_SETERR( err )( "Invalid element handle", MsqError::INVALID_ARG );
        return;
    }

    unsigned i, numvert;

    numvert = TopologyInfo::corners( elementList[index].topology );
    if( numvert )
        for( i = numvert; i < elementList[index].connectivity.size(); ++i )
            --vertexList[elementList[index].connectivity[i]].midcount;

    elementList[index].topology = type;

    numvert = TopologyInfo::corners( elementList[index].topology );
    if( numvert )
        for( i = numvert; i < elementList[index].connectivity.size(); ++i )
            ++vertexList[elementList[index].connectivity[i]].midcount;
}

const std::vector< size_t >& MeshImplData::element_connectivity( size_t index, MsqError& err ) const
{
    if( !is_element_valid( index ) )
    {
        MSQ_SETERR( err )( "Invalid element handle", MsqError::INVALID_ARG );
        return dummy_list;
    }

    return elementList[index].connectivity;
}

const std::vector< size_t >& MeshImplData::vertex_adjacencies( size_t index, MsqError& err ) const
{
    if( !is_vertex_valid( index ) )
    {
        MSQ_SETERR( err )( "Invalid vertex handle", MsqError::INVALID_ARG );
        return dummy_list;
    }

    return vertexList[index].adjacencies;
}

void MeshImplData::clear()
{
    vertexList.clear();
    elementList.clear();
    deletedVertexList.clear();
    deletedElementList.clear();
    haveSlavedFlags = false;
}

void MeshImplData::allocate_vertices( size_t count, MsqError& err )
{
    if( vertexList.size() )
    {
        MSQ_SETERR( err )( MsqError::INVALID_STATE );
        return;
    }

    vertexList.resize( count );
}

void MeshImplData::allocate_elements( size_t count, MsqError& err )
{
    if( elementList.size() )
    {
        MSQ_SETERR( err )( MsqError::INVALID_STATE );
        return;
    }

    elementList.resize( count );
}

void MeshImplData::set_vertex_coords( size_t index, const Vector3D& coords, MsqError& err )
{
    if( !is_vertex_valid( index ) )
    {
        MSQ_SETERR( err )( "Invalid vertex handle", MsqError::INVALID_ARG );
        return;
    }

    vertexList[index].coords = coords;
}

void MeshImplData::reset_vertex( size_t index, const Vector3D& coords, bool fixed, MsqError& err )
{
    if( index >= vertexList.size() )
    {
        MSQ_SETERR( err )( "Invalid vertex handle", MsqError::INVALID_ARG );
        return;
    }

    Vertex& vert = vertexList[index];

    if( !vert.adjacencies.empty() )
    {
        MSQ_SETERR( err )( "Cannot overwrite referenced vertex", MsqError::INVALID_STATE );
        return;
    }

    vert.coords = coords;
    vert.fixed  = fixed;
    vert.valid  = true;
}

void MeshImplData::reset_element( size_t index,
                                  const std::vector< long >& vertices,
                                  EntityTopology topology,
                                  MsqError& err )
{
    clear_element( index, err );MSQ_ERRRTN( err );
    set_element( index, vertices, topology, err );MSQ_ERRRTN( err );
}

void MeshImplData::reset_element( size_t index,
                                  const std::vector< size_t >& vertices,
                                  EntityTopology topology,
                                  MsqError& err )
{
    clear_element( index, err );MSQ_ERRRTN( err );
    set_element( index, vertices, topology, err );MSQ_ERRRTN( err );
}

void MeshImplData::clear_element( size_t index, MsqError& err )
{
    if( index >= elementList.size() )
    {
        MSQ_SETERR( err )( "Invalid element handle", MsqError::INVALID_ARG );
        return;
    }

    unsigned numvert = TopologyInfo::corners( elementList[index].topology );
    if( numvert )
        for( unsigned i = numvert; i < elementList[index].connectivity.size(); ++i )
            --vertexList[elementList[index].connectivity[i]].midcount;

    std::vector< size_t >& conn = elementList[index].connectivity;
    for( std::vector< size_t >::iterator iter = conn.begin(); iter != conn.end(); ++iter )
    {
        std::vector< size_t >& adj = vertexList[*iter].adjacencies;
        for( std::vector< size_t >::iterator iter2 = adj.begin(); iter2 != adj.end(); ++iter2 )
        {
            if( *iter2 == index )
            {
                adj.erase( iter2 );
                break;
            }
        }
    }
    conn.clear();
}

void MeshImplData::set_element( size_t index,
                                const std::vector< long >& vertices,
                                EntityTopology topology,
                                MsqError& err )
{
    if( sizeof( long ) == sizeof( size_t ) )
        set_element( index, *reinterpret_cast< const std::vector< size_t >* >( &vertices ), topology, err );
    else
    {
        std::vector< size_t > conn( vertices.size() );
        std::copy( vertices.begin(), vertices.end(), conn.begin() );
        set_element( index, conn, topology, err );
    }
}

void MeshImplData::set_element( size_t index,
                                const std::vector< size_t >& vertices,
                                EntityTopology topology,
                                MsqError& err )
{
    if( index >= elementList.size() )
    {
        MSQ_SETERR( err )( "Invalid element handle", MsqError::INVALID_ARG );
        return;
    }

    elementList[index].connectivity = vertices;
    elementList[index].topology     = topology;

    for( std::vector< size_t >::const_iterator iter = vertices.begin(); iter != vertices.end(); ++iter )
    {
        if( !is_vertex_valid( *iter ) )
        {
            MSQ_SETERR( err )( "Invalid vertex handle", MsqError::INVALID_ARG );
            return;
        }

        std::vector< size_t >& adj = vertexList[*iter].adjacencies;
        for( std::vector< size_t >::iterator iter2 = adj.begin(); iter2 != adj.end(); ++iter2 )
            if( *iter2 == index ) return;

        adj.push_back( index );
    }

    unsigned numvert = TopologyInfo::corners( elementList[index].topology );
    if( numvert )
        for( unsigned i = numvert; i < elementList[index].connectivity.size(); ++i )
            ++vertexList[elementList[index].connectivity[i]].midcount;
}

size_t MeshImplData::add_vertex( const Vector3D& coords, bool fixed, MsqError& err )
{
    size_t index;

    if( !deletedVertexList.empty() )
    {
        index = deletedVertexList[deletedVertexList.size() - 1];
        deletedVertexList.pop_back();
        reset_vertex( index, coords, fixed, err );
        MSQ_ERRZERO( err );
    }
    else
    {
        index = vertexList.size();
        vertexList.push_back( Vertex( coords, fixed ) );
    }

    return index;
}

size_t MeshImplData::add_element( const std::vector< long >& vertices, EntityTopology topology, MsqError& err )
{
    size_t index;
    if( !deletedElementList.empty() )
    {
        index = deletedElementList[deletedElementList.size() - 1];
        deletedElementList.pop_back();
    }
    else
    {
        index = elementList.size();
        elementList.resize( elementList.size() + 1 );
    }

    set_element( index, vertices, topology, err );
    MSQ_ERRZERO( err );
    return index;
}

size_t MeshImplData::add_element( const std::vector< size_t >& vertices, EntityTopology topology, MsqError& err )
{
    size_t index;
    if( !deletedElementList.empty() )
    {
        index = deletedElementList[deletedElementList.size() - 1];
        deletedElementList.pop_back();
    }
    else
    {
        index = elementList.size();
        elementList.resize( elementList.size() + 1 );
    }

    set_element( index, vertices, topology, err );
    MSQ_ERRZERO( err );
    return index;
}

void MeshImplData::delete_vertex( size_t index, MsqError& err )
{
    if( !is_vertex_valid( index ) )
    {
        MSQ_SETERR( err )( "Invalid vertex handle", MsqError::INVALID_ARG );
        return;
    }

    vertexList[index].valid = false;
    deletedVertexList.push_back( index );
}

void MeshImplData::delete_element( size_t index, MsqError& err )
{
    clear_element( index, err );MSQ_ERRRTN( err );
    deletedElementList.push_back( index );
}

void MeshImplData::copy_mesh( size_t* vertex_handle_array,
                              size_t* element_handle_array,
                              size_t* element_conn_offsets,
                              size_t* element_conn_indices )
{
    std::vector< size_t > vertex_map( vertexList.size() );
    size_t vh_index = 0;
    for( size_t v = 0; v < vertexList.size(); ++v )
    {
        if( vertexList[v].valid
#ifdef SEPARATE_MID_NODES
            && vertexList[v].midcount < vertexList[v].adjacencies.size()
#endif
        )
        {
            vertex_handle_array[vh_index] = v;
            vertex_map[v]                 = vh_index;
            ++vh_index;
        }
        else
        {
            vertex_map[v] = vertexList.size();
        }
    }

    size_t offset = 0;
    for( size_t e = 0; e < elementList.size(); ++e )
    {
        Element& elem = elementList[e];
        size_t cl;
#ifdef SEPARATE_MID_NODES
        cl = TopologyInfo::corners( elem.topology );
        if( !cl )
#endif
            cl = elem.connectivity.size();
        if( cl )
        {
            *element_handle_array = e;
            ++element_handle_array;

            *element_conn_offsets = offset;
            ++element_conn_offsets;
            offset += cl;

            std::vector< size_t >::iterator conn = elem.connectivity.begin();
            std::vector< size_t >::iterator end  = conn + cl;
            while( conn != end )
            {
                *element_conn_indices = vertex_map[*conn];
                ++element_conn_indices;
                ++conn;
            }
        }
    }
    *element_conn_offsets = offset;
}

void MeshImplData::copy_higher_order( std::vector< size_t >& mid_nodes,
                                      std::vector< size_t >& vertices,
                                      std::vector< size_t >& vertex_indices,
                                      std::vector< size_t >& index_offsets,
                                      MsqError& err )
{
    mid_nodes.clear();
    vertices.clear();
    vertex_indices.clear();
    index_offsets.clear();

    // Create a map of from vertex handle to index in "vertices"
    // Use vertexList.size() to mean uninitialized.
    size_t v;
    std::vector< size_t > vert_map( vertexList.size() );
    for( v = 0; v < vertexList.size(); ++v )
        vert_map[v] = vertexList.size();

    // Loop over all mid-side vertices
    for( v = 0; v < vertexList.size(); ++v )
    {
        const Vertex& vert = vertexList[v];

        // Not a mid-side vertex, skip it
        if( !vert.valid || !vert.midcount ) continue;

        // Populate "verts" with the handles of all adjacent corner vertices
        assert( vert.adjacencies.size() );  // shouldn't be able to fail if vert.midcount > 0
        int elem_indx = vert.adjacencies[0];
        Element& elem = elementList[elem_indx];

        // Find index of node in elem's connectivity list
        unsigned index;
        for( index = 0; index < elem.connectivity.size(); ++index )
            if( elem.connectivity[index] == v ) break;
        if( index == elem.connectivity.size() )
        {
            MSQ_SETERR( err )( "Inconsistent data.", MsqError::INTERNAL_ERROR );
            return;
        }

        // Given the index in the element's connectivity list,
        // get the side of the element containing the mid-node.
        unsigned side_dim, side_num;
        TopologyInfo::side_number( elem.topology, elem.connectivity.size(), index, side_dim, side_num, err );MSQ_ERRRTN( err );

        if( !side_dim )  // Not a mid-side node
        {
            MSQ_SETERR( err )( MsqError::INVALID_STATE, "Improperly connected mesh." );
            return;
        }

        // Get the adjacent corner vertices from the element side.
        unsigned num_corners;
        const unsigned* corner_indices =
            TopologyInfo::side_vertices( elem.topology, side_dim, side_num, num_corners, err );MSQ_ERRRTN( err );

        // Add the mid-side node to the output list
        mid_nodes.push_back( v );
        // Store offset at which the indices of the corner
        // vertices adjacent to this mid-side node will be
        // stored in "vertex_indices".
        index_offsets.push_back( vertex_indices.size() );
        // For each adjacent corner vertex, if the vertex is not
        // already in "vertices" add it, and add the index to
        // the adjacency list for this mid-side node.
        for( unsigned i = 0; i < num_corners; ++i )
        {
            size_t vert_idx = elem.connectivity[corner_indices[i]];
            assert( is_vertex_valid( vert_idx ) );

            if( vert_map[vert_idx] == vertexList.size() )
            {
                vert_map[vert_idx] = vertices.size();
                vertices.push_back( vert_idx );
            }
            vertex_indices.push_back( vert_map[vert_idx] );
        }
    }
    index_offsets.push_back( vertex_indices.size() );
}

bool MeshImplData::is_mid_node( size_t index ) const
{
    return is_vertex_valid( index ) && vertexList[index].midcount > 0;
}

bool MeshImplData::is_corner_node( size_t index ) const
{
    return is_vertex_valid( index ) && vertexList[index].midcount < vertexList[index].adjacencies.size();
}

void MeshImplData::all_vertices( std::vector< size_t >& list, MsqError& ) const
{
    list.clear();
    for( size_t idx = 0; idx < vertexList.size(); ++idx )
        if( vertexList[idx].valid ) list.push_back( idx );
}

void MeshImplData::all_elements( std::vector< size_t >& list, MsqError& ) const
{
    list.clear();
    for( size_t idx = 0; idx < elementList.size(); ++idx )
        if( !elementList[idx].connectivity.empty() ) list.push_back( idx );
}

void MeshImplData::get_adjacent_elements( std::vector< size_t >::const_iterator node_iter,
                                          std::vector< size_t >::const_iterator node_end,
                                          std::vector< size_t >& elems,
                                          MsqError& err )
{
    if( node_iter == node_end || !is_vertex_valid( *node_iter ) )
    {
        MSQ_SETERR( err )( MsqError::INVALID_ARG );
        return;
    }

    // Get list of elements adjacent to first node
    elems = vertexList[*node_iter].adjacencies;

    // For each aditional node, intersect elems with elements adjacent to node
    for( ++node_iter; node_iter != node_end; ++node_iter )
    {
        std::vector< size_t >::iterator elem_iter = elems.begin();
        while( elem_iter != elems.end() )
        {
            std::vector< size_t >::const_iterator adj_iter      = vertexList[*node_iter].adjacencies.begin();
            const std::vector< size_t >::const_iterator adj_end = vertexList[*node_iter].adjacencies.end();
            for( ; adj_iter != adj_end; ++adj_iter )
                if( *elem_iter == *adj_iter ) break;

            if( adj_iter == adj_end )
            {
                *elem_iter = elems[elems.size() - 1];
                elems.pop_back();
            }
            else
            {
                ++elem_iter;
            }
        }
    }
}

bool MeshImplData::has_adjacent_elements( size_t elem, const std::vector< size_t >& nodes, MsqError& err )
{
    std::vector< size_t > adj_elems;
    const unsigned dim = TopologyInfo::dimension( elementList[elem].topology );
    get_adjacent_elements( nodes.begin(), nodes.end(), adj_elems, err );

    std::vector< size_t >::iterator iter;
    for( iter = adj_elems.begin(); iter != adj_elems.end(); ++iter )
        if( *iter != elem && TopologyInfo::dimension( elementList[*iter].topology ) == dim ) break;

    return iter != adj_elems.end();
}

void MeshImplData::skin( std::vector< size_t >& sides, MsqError& err )
{
    std::vector< size_t > side_nodes;

    // For each element in mesh
    for( size_t elem = 0; elem < elementList.size(); ++elem )
    {
        if( !is_element_valid( elem ) ) continue;

        // For each side of the element, check if there
        // are any adjacent elements.
        const EntityTopology topo   = elementList[elem].topology;
        std::vector< size_t >& conn = elementList[elem].connectivity;
        switch( topo )
        {
                // For normal elements (not poly****)
            default: {
                unsigned num = TopologyInfo::sides( topo );
                unsigned dim = TopologyInfo::dimension( topo ) - 1;
                // For each side
                for( unsigned side = 0; side < num; ++side )
                {
                    // Get list of vertices defining the side
                    unsigned count;
                    const unsigned* indices = TopologyInfo::side_vertices( topo, dim, side, count, err );MSQ_ERRRTN( err );
                    side_nodes.clear();
                    for( unsigned k = 0; k < count; ++k )
                        side_nodes.push_back( conn[indices[k]] );

                    // If no adjacent element, add side to output list
                    bool adj = has_adjacent_elements( elem, side_nodes, err );MSQ_ERRRTN( err );
                    if( !adj )
                    {
                        sides.push_back( elem );
                        sides.push_back( side );
                    }
                }
            }
            break;

            case POLYGON: {
                for( unsigned side = 0, next = 1; next < conn.size(); ++side, ++next )
                {
                    side_nodes.clear();
                    side_nodes.push_back( conn[side] );
                    side_nodes.push_back( conn[next] );

                    // If no adjacent element, add side to output list
                    bool adj = has_adjacent_elements( elem, side_nodes, err );MSQ_ERRRTN( err );
                    if( !adj )
                    {
                        sides.push_back( elem );
                        sides.push_back( side );
                    }
                }
            }
            break;

            case POLYHEDRON: {
                for( unsigned side = 0; side < conn.size(); ++side )
                {
                    side_nodes = elementList[conn[side]].connectivity;

                    // If no adjacent element, add side to output list
                    bool adj = has_adjacent_elements( elem, side_nodes, err );MSQ_ERRRTN( err );
                    if( !adj )
                    {
                        sides.push_back( elem );
                        sides.push_back( side );
                    }
                }
            }
            break;
        }  // switch(topo)
    }      // for (elementList)
}

MeshImplVertIter::~MeshImplVertIter() {}

void MeshImplVertIter::restart()
{
    index = 0;
    if( !mesh->is_vertex_valid( index ) ) operator++();
}

void MeshImplVertIter::operator++()
{
    ++index;
    while( index < mesh->max_vertex_index() && ( !mesh->is_vertex_valid( index ) || !mesh->is_corner_node( index ) ) )
        ++index;
}

Mesh::VertexHandle MeshImplVertIter::operator*() const
{
    return reinterpret_cast< Mesh::VertexHandle >( index );
}

bool MeshImplVertIter::is_at_end() const
{
    return index >= mesh->max_vertex_index();
}

MeshImplElemIter::~MeshImplElemIter() {}

void MeshImplElemIter::restart()
{
    index = 0;
    if( !mesh->is_element_valid( index ) ) operator++();
}

void MeshImplElemIter::operator++()
{
    ++index;
    while( index < mesh->max_element_index() && !mesh->is_element_valid( index ) )
        ++index;
}

Mesh::ElementHandle MeshImplElemIter::operator*() const
{
    return reinterpret_cast< Mesh::ElementHandle >( index );
}

bool MeshImplElemIter::is_at_end() const
{
    return index >= mesh->max_element_index();
}

}  // namespace MBMesquite
